[gmx-users] bond sequence and improper angles

[Justin Lemkul]

On 3/6/18 8:33 AM, Andrea Spitaleri wrote:
> Hi there,
>
> I have a very quick question: in rtp file the improper definition 
> depends on the bond sequence? I mean:
>
> [ bonds ]
>
> C1 C2
> C2 C3
> C3 C4
>
> [ impropers ]
>
> C1 C4 C3 C2
>
> is identical to this:
>
> [ bonds ]
>
> C2 C1  ; swap
> C3 C2  ; swap
> C3 C4
>
> [ impropers ]
>
> C1 C4 C3 C2
>
> No info in the manual.
>

The order of the bonds is irrelevant. The order of the atoms in the 
[impropers] directory is important, as the first entry is the atom 
around which the improper acts, and the other three determine the 
relevant planes.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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